-
Notifications
You must be signed in to change notification settings - Fork 0
/
nextflow.config
64 lines (56 loc) · 2.36 KB
/
nextflow.config
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
// Daniel Stribling | ORCID: 0000-0002-0649-9506
// Renne Lab, University of Florida
// hkref (hybkit Reference) Project : http://www.github.com/RenneLab/hkref
// Hybkit Project : http://www.github.com/RenneLab/hybkit
// Pipeline Details
manifest {
author = 'Daniel Stribling, Rolf Renne'
defaultBranch = 'master'
description = """\
Hybkit Reference (hkref) : A database and preparation pipelne for preparing
a fasta sequence library for analysis of hybrid sequences generated through
RNA-ligation and sequencing methods such as Quick Crosslinking, Ligation,
and Sequencing of Hybrids experiments.
""".stripIndent()
//doi
//homePage = 'http://www.RenneLab.com'
mainScript = 'hkref_build.nf'
name = 'hkref'
nextflowVersion = '>=20.10.6'
version = '1.0'
}
params.user_email = "${USER_EMAIL}"
process.maxRetries = 3
//singularity.enabled = true
//singularity.cacheDir = "${projectDir}/envs_singularity"
conda.cacheDir = "${projectDir}/envs_conda"
conda.enabled = true
params {
// -- Database Info:
build_dbs = [
'hsa-110-dev1_full': [
'db_settings': "${projectDir}/settings_db_hsa.yaml",
'ensembl_sets': ['protein_coding', 'lncRNA', 'rRNA', 'tRNA', 'other'],
//'ensembl_sets': ['test'],
//'ensembl_sets': ['protein_coding'],
'ext_dbs': ['tRNA'],
'genbank_trnas': true,
],
'hsa-110-dev1_sel': [
'db_settings': "${projectDir}/settings_db_hsa.yaml",
'ensembl_sets': ['protein_coding', 'lncRNA', 'other'],
//'ensembl_sets': ['test'],
//'ensembl_sets': ['protein_coding'],
//'ext_dbs': ['tRNA'],
'ext_dbs': [],
'genbank_trnas': false,
]
]
settings_output = "${projectDir}/settings_output.yaml"
settings_project = "${projectDir}/settings_project.yaml"
// -- Process Environment Variables
python_conda = 'bioconda::pybiomart=0.2.0 pandas=1.3.5 bioconda::biothings_client=0.2.6 conda-forge::biopython=1.79 pyyaml=6.0 natsort=7.1.1'
seqkit_conda = 'conda-forge::biopython=1.79 bioconda::seqkit=2.5.1 pyyaml=6.0'
cluster_conda = 'conda-forge::biopython=1.79 bioconda::cd-hit=4.8.1 bioconda::blast=2.14.1'
mask_conda = 'conda-forge::libgcc-ng=9.3 bowtie2=2.4.4 bioconda::bedtools=2.30.0 bioconda::bedops=2.4.39'
}